rki-mf1/clean

Issues

• Duplicated entries in intermediate BAM file

  #107 opened 4 months ago by hoelzer
  0

• Summary file for number and proportion of mapped and unmapped reads

  #105 opened 4 months ago by ayoraind
  2

• Add curl option for downloading available references

  #104 opened 4 months ago by ayoraind
  5

• Replace minimap2 with another mapper for short-read data?

  #102 opened 5 months ago by hoelzer
  3

• add genome size estimation

  #5 opened 5 months ago by hoelzer
  1

• Use human GRCh38 T2T genome as new option

  #57 opened 5 months ago by hoelzer
  5

• Increase memory when bbduk runs out

  #82 opened a year ago by MarieLataretu
  2

• Provide an option to skip QC steps

  #89 opened 5 months ago by matthuska
  0

• Bump GitHub actions to handle warning re Node.js 16 to 20 transition

  #91 opened 5 months ago by matthuska
  0

• Differences in MultiQC report between BBDUK and minimap2 runs

  #98 opened 7 months ago by hoelzer
  0

• Improve output report/summary

  #84 opened a year ago by matthuska
  1

• Fix intermittant conda-related failures of GitHub Actions

  #93 opened 8 months ago by matthuska
  0

• bam files instead of fastq?

  #88 opened 9 months ago by selmapichot
  1

• Concat contamination error on SLURM/Singularity

  #86 opened 10 months ago by hoelzer
  3

• Using user defined host genome

  #85 opened a year ago by haotianteng
  2

• Add tests that use real sequencing data as input

  #83 opened a year ago by matthuska
  0

• make contig names unique when concatenating

  #44 opened a year ago by MarieLataretu
  2

• add a keep option

  #55 opened a year ago by MarieLataretu
  6

• Reduce size of temp files and/or remove temp files

  #58 opened a year ago by mw55309
  7

• FASTA host file does not work in IGV

  #74 opened a year ago by hoelzer
  15

• Container for bedtools and samtools ("bed_samtools") is missing

  #68 opened a year ago by matthuska
  1

• Add SARS-CoV-2 as a species

  #62 opened a year ago by matthuska
  1

• samtools error caused by ncurses version information

  #60 opened a year ago by imogen-foote
  5

• problem when input files end with clean

  #46 opened a year ago by MarieLataretu
  1

• do concat_contamination only once

  #47 opened a year ago by MarieLataretu
  0

• add --split-prefix to minimap2

  #45 opened a year ago by MarieLataretu
  0

• add idxstats to multiqc

  #42 opened a year ago by MarieLataretu
  0

• Publication about broadly contaminating viruses

  #56 opened 2 years ago by hoelzer
  0

• check for newlines when concat fastas

  #52 opened 3 years ago by hoelzer
  6

• reference index file incomplete

  #40 opened 3 years ago by MarieLataretu
  1

• minimap2 additional filter

  #23 opened 3 years ago by hoelzer
  3

• ONT clean minimap2/samtools error "query name too long"

  #35 opened 4 years ago by hoelzer
  7

• MultiQC support

  #22 opened 4 years ago by hoelzer
  5

• bbduk gets bamboozled if input file names contain `clean`

  #25 opened 4 years ago by MarieLataretu
  0

• Error with input FASTA via --own

  #29 opened 4 years ago by hoelzer
  1

• Output also a FASTA index so that the BAMs can be actually used

  #30 opened 4 years ago by hoelzer
  1

• Encapsulate read renaming

  #19 opened 4 years ago by MarieLataretu
  0

• (profile) parameter not overwritten by additional custom config

  #24 opened 4 years ago by MarieLataretu
  0

• bbduk quality encoding change

  #26 opened 4 years ago by lisa-mariebarf
  4

• ENA Upload Extension

  #21 opened 5 years ago by hoelzer
  0

• Illumina single-end data

  #4 opened 5 years ago by hoelzer
  7

• test installation via conda/docker

  #7 opened 5 years ago by hoelzer
  2

• add statistics to log file

  #10 opened 5 years ago by MarieLataretu
  9

• Missing log.txt file for bbduk

  #15 opened 5 years ago by hoelzer
  0

• --list not working

  #13 opened 5 years ago by MarieLataretu
  4

• add control sequences to the repository

  #6 opened 5 years ago by hoelzer
  0

• replace bowtie2 short-read clean w/ bbduk

  #9 opened 5 years ago by hoelzer
  8

• cloud storage via db_preload.exists() does not work for bowtie2 index

  #8 opened 5 years ago by hoelzer
  1

• Ont control cleaning

  #3 opened 5 years ago by hoelzer
  2

• user passed host genome

  #2 opened 5 years ago by hoelzer
  0